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Citric Acid Cycle Question

I'm in the process of learning the steps in the citric acid cycle, and when looking at the cycle I was curious if certain intermediates can be straight up inserted into the cycle or if they need to go through the full thing in order to be used correctly?

For example, fumarate to malate via fumarase - if we consume food with malate in it and have a higher than normal concentration of malate in our body, will fumarase not need to be used, let alone all the other preceding steps in the cycle?

Actually I guess the downside of skipping all those steps would be missing out on all the NADH, ATP, and FADH2 that are produced beforehand.....but still curious if certain components can be inserted into the cycle?!

My only background on this topic is intro biochem so idek if this question makes sense

02:23 UTC


What is the role of caspases in aging?

19:37 UTC


Am I the only one genuinely tweaking whenever coming across misinformation like this?

I cant stand it. This happens so much. Im basically seething in my chair reading these comments. I know these people mean no harm but they really do harm by spreading around misinformation like this. Antibacterial/microbial is NOT the same obviously 😭. This wont do anything against viral infection but they swear it ”works” like wdym your body is just fighting off the flu lol, garlic & honey or not.

17:28 UTC


Any good books for careers in Biochemistry?


I'm working on an internship and one of my tasks is to create a list of college-level books that talk about careers in Chemistry and Biochemistry such as:

What kind of careers are in biochem?

How to do the jobs in such fields?

What tests are required for grad school?

Does anyone have any suggestions?

16:27 UTC


Help understanding an old exam question


Not sure where else to ask but I figured you guys might know. I’m studying for my country’s biochem entrance exams and I’m looking at old exams and I’m stuck on a question. I’ll try to translate accurately:

”Carbonic anhydrase catalyses the conversion of carbon dioxide and water into carbonic acid which in turn creates bicarbonate and hydrogen ions. The enzyme is quite fast, and its kcat=4,0•105s⁻¹ (reactions per second). How long does it take for the enzyme to process one substrate molecule?”

The answer is very simply written as ”t=1/kcat=1/4•105s⁻¹=2.5•10⁻⁶s=2.5 µs”

I don’t understand how this is calculated and the answer only leaves me with more questions. Can anyone help?

15:23 UTC


There was a mistake in my exam and my professor is not giving me the points back

The question was asking something like which of the following best represents the net equation of the pentose phosphate pathway when 5 carbon sugars are needed.

The correct answer to the question should be: glucose-6-P + H2O + 2 NADP -> CO2 + pentose-5-P + 2 NADPH This is even in the slides. But this right answer was not one of the choices. Instead the choices were something like:

a. Wrong b. glucose-6-P + 2 H2O + 2 NADP -> CO2 + pentose-5-P + 2 NADPH c. Wrong d. Wrong e. None of the above

Answer b is also wrong because it says that the PPP uses two H2O molecules. Choice b. breaks the law of conservation of mass. Therefore, the correct answer should be e. None of the above.

It’s like asking “which of the following equations best represents the formula 2 + 1 = 3?” And the answer choices are:

a. 2 + 2 = 3 b. 2 + 2 = 5 c. 2 + 1 = 4 d. 2 + 1 = 5 e. None of the above

e. Should be the answer because none of the choices are accurate.

It doesn’t seem fair to me to lose points on a question where the answer choice is incorrect, and it breaks one of the fundamental laws of the universe.

My professor is not conceding. He says that besides the number of water molecules, that was the answer. Am I in the wrong in this situation? It seems like the number of water molecules should be crucial. I don’t know what to do at this point.

14:19 UTC


Could I still do a masters in marine biology with a bachelors degree in biochemistry?

13:42 UTC


Last year of degree. What now?

So I'm finishing a bachelors degree on Biochemistry and I'm a bit lost about my future right now. I don't know whether to start a masters degree and pursue a doctorate even though my grades aren't really good or start working right away. About the masters, I was thinking maybe Celular and Molecular Biology and get a part-time job to get a doctorate. If I don't get into a masters degree, what job could I apply for?? Thanks in advance.

07:08 UTC


Mycelium substitutes

I’m working on a biodesign project and would love to propose a new innovative idea. I’m well aware of the dimensions mycelium offers and its durability and flexibility on creating a great sources of alternatives for many environmental damaging elements. However, due to the constant reports on mycelium I would like to try to work with a new material that is similar to mycelium but IS NOT mycelium. I read and see about it everywhere I would just like to try and research something new but still just as dependable and innovative.

So basically what’s a good alternative or substitute for mycelium? Something that still has all the good attributes of mycelium?

05:55 UTC


Differences in ligand interactions between PDB with hydrogens and a PDB without hydrogens in Biovia Discovery Studio


I'm trying to analyze my ligand-bound crystal structures with Biovia Discovery studio and I'm seeing differences between two cases.

I first found the ligand interactions of a group of PDBs which don't have hydrogens. These include everything from hydrogen bonding to pi-pi interactions to alkyl-alkyl to pi-sigma. This is case 1.

The free version of the program also includes the possibility of applying a dreiding-like forcefield on the structure which changes the structure slightly. I did the interaction search again but the list changsd drastically.

It's not that it found something that doesn't make sense but that it removed a large chunk of interactions in case 1. Primarily, a lot of the hydrogen bonds and practically all the pi-sigma bonds found in case 1 were removed. This is case 2.

At first I thought that the dreiding-like forcefield was correcting some severe mistakes in my PDB refinement but it turns out that the problem isn't the forcefield but the hydrogens added. If you remove the hydrogens added from the structure you get something that looks like the first case interactions (albeit still different).

So my question is, should I use the interactions from case 1? or case 2? or should I combine the two cases' interactions?

Additionally, the adding of hydrogens in this program adds hydrogens to the water molecules in the binding pocket of the protein. These ARE involved in interactions but adding the hydrogens limits the found interactions heavily here. Perhaps this is a third case, add hydrogens but remove them from water.

A fourth possible case us to apply the dreiding without typing the PDB and adding hydrogens but I'm not sure the forcefield works without typing.

What do you think is most correct and accurate?

Forgot to mention this but the analyzed PDBs comprise both crystal structures and models based on the crystal structures.

17:52 UTC


Any recommendations for Biochemistry buisness related jobs?

Hello! I am a PhD student in biochemistry who is planning to master out. I haven’t been so happy in the program and feel like it’s time to leave. I am looking into mastering out next year once I am able. However I want to have a plan before i pull the trigger. I have decided that i do not wanna teach or work in a lab for the rest of my life. I am thinking to take more the business/ management route instead along with putting my masters into work. I was wondering if anyone has taken such route and what opportunities should i look mostly to?

Any job or position recommendations that I would he qualified for?

23:14 UTC


Mathematical expression for Kd for 1:2 binding? (antibody-protein binding)

Hi all, could anybody explain or demonstrate the derivation for the mathematical expression for the dissociation constant, Kd, for binding that happens with a 1:2 stoichiometry? (in this case, for an antibody that has 2 binding sites for its specific protein, let's assume both binding sites are independent and that there is no form of cooperativity/allosteric effects)

The typical expression for Kd - ie the concentration at which 50% of one of the binding partners (the one not in excess in a titration experiment) is bound - is straightforward to derive and I can do it no problem, but it is based on a 1:1 binding system. What does the equivalent expression for a 1:2 binding stoichiometry look like?

Thanks in advance!

16:17 UTC


Apr 10: Education & Career Questions

Trying to decide what classes to take?

Want to know what the job outlook is with a biochemistry degree?

Trying to figure out where to go for graduate school, or where to get started?

Ask those questions here.

1 Comment
15:01 UTC


Molybdenum (Mo) and Nitrate (NO3)

11:02 UTC


Biochem vs Biotech

I’m a current university student wanting to switch to either biotech or Biochem, looking to go into research after I graduate. Which bachelors degree do you guys think is more applicable and broad? A more broad (but still usable) degree interests me more so I can go into different fields if I wish to.

I’ve heard a lot of differing opinions and I’m lost right now :(

Thank you:)

07:31 UTC


What jobs can you get with only a bachelors degree in Biochemistry?

I am a first year biochem student in Alberta, Canada. Just wondering what the job options are with just the degree. Also willing to relocate if some job markets are better than others.

Additionally, if you have any experience on the job search with and without higher education please let me know your thoughts.

05:25 UTC


Ghosted after interviews?

I’ve had three internship interviews and one screening interview. I’ve been ghosted by all of them but one of the regular interviews. Is this normal?

01:32 UTC


Schiff base formation via amino acid side chain

19:56 UTC


Should I Shadow a Doctor for Grad School?

I'm a biochem major looking to go to grad school and work in drug development. Would it be beneficial to shadow a doctor relating to my desired field of drug research (endocrinology)? I know this is more of a pre-med thing and that research is ideal in my case. However, I don't have enough time to do a research internship over my break.

18:51 UTC


Second Semester Student Trying to Get Practical Transferrable Skills

Good Afternoon,

I'm finishing my second semester at a local community college. My last semester I did Principles of Chem I with Lab and Calc 1 and am currenlty finishing up my second semester. Overall, I'm a solid B student. Long term my plan is to transfer to a state school and earn a bachelors in Biochemistry. I initially chose biochemistry because I wanted to be able to apply myself to a subject I am not familiar with and be able to apply it usefully. Secondly was to be ready for two alternate career paths. One being a job in Biostatistics. A second would be to apply to PA school after earning the bachelors. I know it sounds blocky but it is just the initial long term objective.

Currently I am looking for the best way to get work experience outside of college lab work. I feel I need more exposure because Our labs are only once a week. Should I communicate directly with the school I am planning to transfer to in the fall or should I look into local entry level jobs? If I am a B average student this early on am I just wasting my time?

18:43 UTC


Cell-to-cell Propagation of Aβ and TAU proteins in AD.

I’m struggling to find an explanation for the propagation of Aβ and TAU proteins in AD. I’m trying to make a clear explanation for a project of mine, but I feel a little flooded. There is a lot of articles talking about the propagation, but I can’t find one that focuses more on the biochemistry aspect of it.

Here’s what I got for now:

As shown by research made on mice, regarding Aβ and TAU injections in the brain, AD progresses as the pathological proteins Aβ and TAU transmit themselves from neuron to neuron, slowly killing them. On the brain scale, it usually follows the same pattern, allowing for the staging of AD when looking at the spread of hyperphosphorylated TAU proteins in the brain’s grey matter. This is caleld Braak staging.

But on the cell scale, their propagation mainly takes place as one of 3 ways:

  • Exosome-mediated transmission, where exosomes containing various proteins and nucleic acids, and our pathological proteins, is released from the cell and transmited to neighboring neurons (how ?).

  • Synaptic transmission, where neurons communicate by exchanging neurotransmitters, ions, etc. It has been shown that Aβ and TAU proteins are able to be transmitted from one synapse to the other, via vesicles (other way ? how ?).

  • Glia-related transmission, these cells are in contact with multiple neurons, and can be the way of transit from one neuron to the other (how ? To what extent ?).

  • ???

Also, do you know about any new research and treatments in the work that could be interesting to talk about ?

17:01 UTC


Liver and aminoacids metabolism


There’s this interesting information that I can’t quite understand.

In Marks’ biochemistry book (clinical aspects), it says that the liver CAN ONLY use methione to make propionyl-CoA. In other words, it CANNOT use valine or isoleucine to make succinyl-CoA. So, why is that? Does it lack a crucial enzyme?

The internet hasn’t been quite helpful, apart from telling me that extrahepatic tissues are much better at metabolising branched aminoacids. Now obviously that is something I can remember, but I do want to understand why that is.

I know that branched aminoacids (Leu, Ile, Val) are pretty good at providing energy via succinyl-CoA and then Krebs’ cycle (so, muscles).

Thanks in advance :)

16:38 UTC


Rationalizing why fatty acids are apparently non-glucogenic

I teach metabolism to undergraduates. I'm also a metabolic biochemist. In my opinion, one of the many fallacies that undergraduates are told by their textbooks is that even-numbered fatty acids are not glucogenic -- that is, fatty acids cannot be used to produce glucose via gluconeogenesis.

I've always hated this statement. Obviously, anyone can see that fatty acids can enter the citric acid cycle as acetyl-CoA, and proceed through all steps until they reach oxaloacetate. Oxaloacetate can be decarboxylated and phosphorylated to phosphoenolpyruvate via PEPCK, and phosphoenolpyruvate can proceed through the remainder of gluconeogenesis. Therefore, if I radiolabel the carbon atoms in a fatty acid, is it not possible for some of the labeled carbons to be found in glucose via this exact pathway?

I realize it is a very indirect way to obtain glucose compared to, say, alanine or aspartate. That being said, the citric acid cycle is recognized as anapleurotic (also from a textbook standpoint), so, why are fatty acids considered non-glucogenic in such a black and white manner?

How do I rationalize this undergraduates who are clever enough to overlay these metabolic pathways and see that, indeed, it is possible to get from an even-numbered fatty acid to glucose.

ADDENDUM: it would seem that it's a quirk of terminology. While the carbon atoms in a fatty acid can ultimately be incorporated into glucose and other sugars, the key is that acetyl-CoA derived from fatty acid catabolism cannot alone, stoichiometrically, form new glucose without condensing with oxaloacetate.

13:01 UTC


Can someone please help me with this question?

Which of the following is true regarding te Michaelis-Menten graph?

A) Km is directly proportional to substrate concentration

B) Km is directly proportional to enzyme concentration

C) Km is indirectly proportional to substrate concentration

D) Km has no relation to substrate concentration

Since Km is constant for a particular enzyme-substrate complex, shouldn't the answer be D? But the correct answer is A apparently.

04:21 UTC


Our biochemistry

I want to know how much do we know about our body in terms of what are we made. I know that there are macromolecules as nucleic acid, carbohydrates, proteins and lipids. But do we know every single molecule in our body? Are they all identified?

From what I've heard, there is a project called Human Proteome Project which is until today trying to find out every single protein produced by our genome.

Can you tell how much (in terms of %, approximately) do we know about our body in terms of our biochemistry?

22:12 UTC


People with biochem degrees, what jobs do you have now?

I’m currently a freshman in college, majoring in biochem, trying to get my bachelors. I’m specifically interested in the medical field and would love to know the opportunities you had after graduating or what higher education you sought. I’m trying to avoid taking out loans, but I’m not opposed to it if higher education is worth the cost. I’d love to work in a hospital, but I’m open to other opportunities. Suggestions would be appreciated and thank you for reading. (I’m in the US, but I’m interested in hearing from everyone and how they succeeded in other countries as well!)

18:03 UTC


Apr 08: Weekly Research Plans

Writing a paper?

Re-running an experiment for the 18th time hoping you finally get results?

Analyzing some really cool data?

Start off your week by sharing your plans with the rest of us. å

15:00 UTC


If the cellular concentrations of ATP, ADP, and Pi are 8, 1, and 8 mM, respectively, what is delta G? Is this reaction at equilibrium?

How is the answer -48.8 x 10^3 J/Mol when I'm not given delta G° to plug in for the formula delta G=delta G° + RT lnK? Is ΔG° -48.8 x 10^3 because the reactant ATP of 8 mM and products ADP and Pi with 1 and 8 mM respectively gives a product to reactant ratio of 1 and ln of 1 = 0 and RT * ln(1) = 0 so then is ΔG° -48.8 x 10^3 because RTlnK = 0 which gives the answer ΔG = -48.8 x 10^3?

06:17 UTC


acrylate chemistry

05:39 UTC

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